Method for evaluating multiple different genes of interest

Abstract

It is an object of the present invention to provide, for instance, a method for evaluating a function, such as transforming potential, of multiple different genes of interest, and a method capable of evaluating drug sensitivity of a subject having each gene of interest. The present invention relates to, for instance, a method for evaluating multiple different genes of interest, comprising the steps of: integrating, into host cell genomic DNA, polynucleotides each comprising a tag sequence and a gene of interest or a fragment thereof linked to the tag sequence; mixing a plurality of different host cells having the different polynucleotides integrated therein; culturing the mixed host cells; extracting the genomic DNA from the cultured host cells; quantifying each of the polynucleotides in the extracted genomic DNA based on the tag sequence; and determining a relative cell count of each of the host cells having the respective polynucleotides after the culturing, based on the quantified values for the polynucleotides.

The invention claimed is: 
     
       1. A method for evaluating multiple different genes of interest, comprising the steps of:
 integrating, into host cell genomic DNA, polynucleotides each comprising a tag sequence and a gene of interest or a fragment thereof linked to the tag sequence; 
 mixing a plurality of host cells having the different polynucleotides integrated therein; 
 culturing the mixed host cells; 
 extracting the genomic DNA from the cultured host cells; 
 quantifying each of the polynucleotides in the extracted genomic DNA based on the tag sequence; and 
 determining a relative cell count of each of the host cells having the respective polynucleotides after the culturing, based on the quantified values for the polynucleotides. 
 
     
     
       2. The method according to  claim 1 , wherein the gene of interest includes a reference gene, wherein the method comprises the step of comparing the relative cell count of the host cells after the culturing with a reference value, and wherein the reference value is defined as a relative cell count of a host cell comprising a polynucleotide comprising the reference gene after the culturing. 
     
     
       3. The method according to  claim 2 , further comprising the step of evaluating the gene of interest as having transforming potential, when the relative cell count after the culturing is higher than the reference value. 
     
     
       4. The method according to  claim 2 , wherein
 the culturing is performed under a differentiation-inducing condition, and 
 the method further comprises the step of evaluating the gene of interest as a gene that suppresses the differentiation, when the relative cell count after the culturing is higher than the reference value. 
 
     
     
       5. The method according to  claim 1 , wherein the culturing is performed under a test environment. 
     
     
       6. The method according to  claim 5 , wherein the test environment is in the presence of a test substance. 
     
     
       7. The method according to  claim 6 , wherein the genes of interest is oncogene, wherein the culturing is performed in a presence of an anti-cancer drug, and wherein the method comprises the step of evaluating sensitivity of the oncogene to the anti-cancer drug based on the relative cell count after the culturing. 
     
     
       8. The method according to  claim 7 , wherein the anti-cancer drug is a low-molecular-weight compound and/or an antibody drug. 
     
     
       9. A method for determining an anti-cancer drug, comprising the step of performing the method according to  claim 7  for a plurality of anti-cancer drugs once or multiple times independently to determine an anti-cancer drug effective for the oncogene based on the obtained results of sensitivities to the anti-cancer drugs. 
     
     
       10. The method according to  claim 6 , wherein the gene of interest is an tumor suppressor gene, wherein the host cells are cells deficient in the tumor suppressor gene, and the culturing is performed under treatment which causes the damage to the host cells that can be repaired by the tumor suppressor gene. 
     
     
       11. The method according to  claim 10 , wherein the test substance is a PARP inhibitor. 
     
     
       12. The method according to  claim 1 , wherein the plurality of host cells having the different polynucleotides integrated therein are derived from the same cell line. 
     
     
       13. The method according to  claim 1 , wherein the gene of interest includes a plurality of mutants of one oncogene. 
     
     
       14. The method according to  claim 1 , wherein the gene of interest includes a compound mutation-bearing gene containing a plurality of mutations to a wild-type gene. 
     
     
       15. The method according to  claim 1 , wherein the quantifying step is performed based on read counts obtained by next-generation sequencing. 
     
     
       16. The method according to  claim 1 , wherein the culturing is performed in vivo using a non-human animal.